Abstract
Microbes in ecosystems often develop coordinated metabolic interactions. Therefore, understanding metabolic interdependencies between microbes is critical to deciphering ecosystem function. In this study, we sought to deconstruct metabolic interdependencies in organohalide-respiring consortium ACT-3 containing Dehalobacter restrictus using a combination of metabolic modeling and experimental validation. D. restrictus possesses a complete set of genes for amino acid biosynthesis yet when grown in isolation requires amino acid supplementation. We reconciled this discrepancy using flux balance analysis considering cofactor availability, enzyme promiscuity, and shared protein expression patterns for several D. restrictus strains. Experimentally, 13C incorporation assays, growth assays, and metabolite analysis of D. restrictus strain PER-K23 cultures were performed to validate the model predictions. The model resolved that the amino acid dependency of D. restrictus resulted from restricted NADPH regeneration and predicted that malate supplementation would replenish intracellular NADPH. Interestingly, we observed unexpected export of pyruvate and glutamate in parallel to malate consumption in strain PER-K23 cultures. Further experimental analysis using the ACT-3 transfer cultures suggested the occurrence of an interspecies malate–pyruvate shuttle reconciling a redox imbalance, reminiscent of the mitochondrial malate shunt pathway in eukaryotic cells. Altogether, this study suggests that redox imbalance and metabolic complementarity are important driving forces for metabolite exchange in anaerobic microbial communities.
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Acknowledgments
Support was provided by the Government of Ontario through Genome Ontario SPARK Research Grant. We also acknowledge the BioZone Mass Spectrometry facility for UPLC-ESI-HRMS analyses. We are grateful to the gift of active Dehalobacter restrictus strain PER-K23 culture from Prof. Frank Löffler in University of Tennessee (Knoxville, USA).
Author contributions
E.A.E., R.M., and P.H.W. conceptualized this study. C.H. and K.C. re-constructed the Dehalobacter model. K.C. performed the Flux Balance Analysis. P.H.W. performed the experiments. K.N. performed the organic acid analysis. R.F. performed the LC–MS analysis. P.H.W. and N.V. proposed the mechanism of interspecies malate–pyruvate shuttle. E.A.E., R.M., and P.H.W. wrote this paper with helps from all the authors. All the authors participated in data analysis and discussion.
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Wang, PH., Correia, K., Ho, HC. et al. An interspecies malate–pyruvate shuttle reconciles redox imbalance in an anaerobic microbial community. ISME J 13, 1042–1055 (2019). https://doi.org/10.1038/s41396-018-0333-4
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DOI: https://doi.org/10.1038/s41396-018-0333-4
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